Sudanese activists have blamed the authorities for the deaths of at least three student protesters and are calling for more demonstrations.

Police in Gezira state, an agricultural area south of the capital Khartoum, confirmed two students had been found dead in a canal, and a third was missing, but said there were no signs of violence.

Arab-African Sudan has avoided the mass protests that have swept across much of the Middle East, but rising food prices and other grievances have inspired smaller demonstrations over the last two years.

Students from Darfur - a western region the size of Spain that has been torn by war for nearly a decade - had staged a sit-in at Gezira University demanding an exemption from tuition as they say a presidential decree required, a spokesman for a Darfur student association said.

He said the sit-in was broken up on Wednesday by what he called militias loyal to the ruling National Congress Party. A number of students disappeared and three were found dead on Friday in the canal near the university, he added, asking not to be named.

"We hold the university administration and the ... students of the National Congress Party responsible for the death of these students," he said.

Sudanese youth activist groups including Change Now and Girifna issued statements blaming security forces for the students' deaths and calling for protests.

Small demonstrations erupted across Sudan in June after the government announced cuts to its costly fuel subsidies and other tough austerity measures to contain an economic crisis brought on by last year's secession of oil-producing South Sudan.

The protests calling for the resignation of President Omar Hassan al-Bashir's government petered out after a security crackdown and the start of the Muslim fasting month of Ramadan.

Bashir and other officials are wanted by the International Criminal Court on charges of masterminding war crimes in Darfur - accusations they deny as politically-motivated inventions of hostile Western forces.